I have seen this phenomenon a few times with newer motherboards as you seem to have. The first thing to check is that the disks have the parameters set right. I have often found that the DMA is switched off. Do
or whatever your system disk is and see if using_dma is on. If it's off, try
hdparm -d 1 /dev/hda
and see if you get errors, such as "Operation not permitted".
At boot time, that behavior is controlled by a file /etc/sysconfig/harddisks. The kernel normally reads DMA capability and some other features from the BIOS, but I find that with newer MoBos this is broken somehow, so I had to force values in that file.
Hope it helps,